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2015-1Schrodinger Python API
Package schrodinger :: Package application :: Package desmond :: Module fep_edge_report_maker :: Class FEPEdgeReportMaker
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Class FEPEdgeReportMaker

object --+
         |
        FEPEdgeReportMaker
Instance Methods [hide private]
 
__init__(self, fep_edge_data, basename=None, report_level=0)
This class generates a PDF report for an FEP/REST (+) type of job.
 
_load_modules(self)
 
report(self)
 
_cleanup_temp_files(self)
 
_init_report(self)
 
_replica_exchange_density(self)
 
get_rest_density_plot(self, rest_density_data, legend=True)
 
get_rest_density_img(self, rest_density_data, legend=True)
 
_protein_ligand_report(self)
 
_get_lid_img(self, stats, lig_noh_dict, lig_atom_dict, ligand_st, cutoff=0.2)
 
_get_lid(self, stats, lig_noh_dict, lig_atom_dict, ligand_st, cutoff=0.2)
 
_get_pl_text(self)
 
_get_plot_pl_bar_chart(self, label, data_dict0, data_dict1, nframes)
 
_ligand_report(self)
Generate ligand report
 
_ligand_properties(self)
 
_ligand_rmsd_wrt_protein(self)
 
_get_ligand_wrt_prot_rmsd_text(self)
 
_get_ligand_wrt_prot_rmsd_plot(self, rmsd_l0, rmsd_l1, ts, ts_max)
 
_protein_report(self)
Generates the protein report (RSMD/RSMF for both end-point lambdas).
 
_protein_rmsf(self)
 
_get_protein_rmsf_text(self)
 
_gen_protein_lambda_rmsf_plot(self, rmsf_l0, rmsf_l1)
 
_protein_rmsd(self)
 
_get_protein_rmsd_text(self)
 
_get_protein_lambda_rmsd_plot(self, rmsd_l0, rmsd_l1, ts, ts_max)
 
_get_pair_rmsd_plot(self, val0, val1, ts, ts_max, names, ylabel='RMSD ($\\AA$)', y_inch=2.5)
 
_get_sequence_viewer_image(self)
Generate protein sequence image, given a protein structure Returns a platypus image
 
_free_energy_convergence_profiles(self)
 
_gen_free_energy_convergence_table(self, df_per_replica, dg, bootstrap_std, analytical_std)
 
_gen_free_energy_convergence_plot(self, start_time, end_time, dG_forward, dG_forward_err, dG_reverse, dG_reverse_err, dG_sliding, dG_sliding_err)
 
_reaction_details(self)
 
_ligand_perturbation_details(self)
 
_generate_2d_lig_images(self)
Generate 2d images of the ligands.
 
_generate_aligned_2d_lig_pair(self)
Generate *aligned* 2d images of the ligands.
 
_protein_details(self)
 
get_2d_ligand_image(self, lig_st)
 
_get_2d_ligand_image(self, st)
 
_get_temp_image_fn(self, prefix='')
 
_report_fep_simulation_details(self)
 
error(self, msg)
 
str(self, str_in)
This is to remove the "'s in ARK returned strings enclosed in double quotes

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods [hide private]
 
_lid_add_lig_water_exposed(res_label, sk, ligand_st, lig_noh_dict, ligand_atoms)
 
_lid_add_water_br(res_label, sk, already_added_res_dict, ligand_st, lig_atom_dict, lig_noh_dict, ligand_atoms, opacity)
`res_label' for water-mediated interactions looks like this:...
 
_lid_add_hydrophobic(res_label, sk, already_added_res_dict)
`res_label` for non-specific hydrophobic interactions looks like this:...
 
_lid_add_picat(res_label, sk, already_added_res_dict, lig_atom_dict, ligand_atoms, opacity)
`res_label` for pi-cat interactions looks like this:...
 
_lid_add_pipi(res_label, sk, already_added_res_dict, lig_atom_dict, ligand_atoms, opacity)
`res_label` for pi-pi interactions looks like this:...
 
_lid_add_prot_metal(res_label, sk, already_added_metal_dict, already_added_res_dict, opacity)
`res_label' for metal-protein mediated interactions looks like this:...
 
_lid_add_lig_metal(res_label, sk, already_added_metal_dict, lig_atom_dict, ligand_atoms, opacity)
`res_label' for metal-ligand mediated interactions looks like this:...
 
_lid_add_intramolecular_hb(res_label, sk, ligand_st, lig_atom_dict, lig_noh_dict, ligand_atoms, opacity)
res_label for internal (intramolecular) hydrogen bonds looks like this:...
 
_lid_add_ionic(res_label, sk, already_added_res_dict, lig_noh_dict, ligand_atoms, opacity)
res_label for ionic bonds looks like this:...
 
_lid_add_hbonds(res_label, sk, already_added_res_dict, ligand_st, lig_atom_dict, lig_noh_dict, ligand_atoms, opacity)
res_label for hydrogen bonds looks like this:...
Class Variables [hide private]
  REPORT_LEVELS = {0: 'Basic', 1: 'Secondary', 2: 'All'}
Properties [hide private]
  get_rest_density_text

Inherited from object: __class__

Method Details [hide private]

__init__(self, fep_edge_data, basename=None, report_level=0)
(Constructor)

 

This class generates a PDF report for an FEP/REST (+) type of job. Both Legs of the simulations are processed in the FEPEdgeData and is used by this class to compile a result.

Parameters:
  • fep_edge_data (FEPEdgeData) - Object containing all the data for this report
  • basename (string) - the basename of the file of the PDF report
  • report_level (int) - this class supports different levels of reporting. by default we'll report just the essential info. Secondary information will be shown if requested, this is the information that can be useful in some cases when troubleshooting the FEP job. The final option is to output *all* the information. where all the analysis types that we have can put in the report, however its usefulness is still in question
Overrides: object.__init__

_lid_add_water_br(res_label, sk, already_added_res_dict, ligand_st, lig_atom_dict, lig_noh_dict, ligand_atoms, opacity)
Static Method

  

`res_label' for water-mediated interactions looks like this:
   (0.610, 'B:LEU_52:O', [-7.148, -19.094, -5.2140861], 3702)
   (freq, prot_label, prot_xyz, ligand_aid)

_lid_add_hydrophobic(res_label, sk, already_added_res_dict)
Static Method

  

`res_label` for non-specific hydrophobic interactions looks like this:
 (0.801, 'B:LEU_52', [-5.9, -21.1, -5.4],
                            [3694, 3695, 3696, 3709, 3710, 3711])
    (freq, prot_label, [prot_xyz], fragment_aids)

_lid_add_picat(res_label, sk, already_added_res_dict, lig_atom_dict, ligand_atoms, opacity)
Static Method

  

`res_label` for pi-cat interactions looks like this:
 (0.16, 'B:ARG_77:CZ', [-5.9, -11.1, -5.9], [3698, 3699, 3701, 3702, 3700])
    (freq, prot_label, [prot_xyz], lig_ring_aids)
in case the aromatic group is on the protein, and charged group on the
ligand:
 (1.0, 'B:TYR_99', [13.404797, 3.522047, 15.211519], 2945)
  (freq, prot_label (aromatic) , [prot_xyz], ligand_aid)

_lid_add_pipi(res_label, sk, already_added_res_dict, lig_atom_dict, ligand_atoms, opacity)
Static Method

  

`res_label` for pi-pi interactions looks like this:
 (0.068, 'B:TYR_14', [4.0, -22.1, -8.7], [3698, 3699, 3701, 3702, 3700],
                                                                    0.0)
   (freq, prot_label, [Calpha_xyz], ligand_rings_aid, f2f_fraction)

_lid_add_prot_metal(res_label, sk, already_added_metal_dict, already_added_res_dict, opacity)
Static Method

  

`res_label' for metal-protein mediated interactions looks like this:
 (1.0, 'A:ASP_116:OD1', 1511, [9.3, 17.1, -3.8], 1, [7.4, 16.6, -5.2])
   (freq, prot_label, Calpha_aid, [Calpha_xyz], metal_aid,
                                            metal_label, metal_xyz)

_lid_add_lig_metal(res_label, sk, already_added_metal_dict, lig_atom_dict, ligand_atoms, opacity)
Static Method

  

`res_label' for metal-ligand mediated interactions looks like this:
 (1.0, 'L-FRAG_0:O1754', 1754, [9.4, 16.6, -7.0], 1, [7.4, 16.6, -5.2])
   (freq, lig_label, [ligand_xyz], metal_aid, metal_label, metal_xyz)

_lid_add_intramolecular_hb(res_label, sk, ligand_st, lig_atom_dict, lig_noh_dict, ligand_atoms, opacity)
Static Method

  

res_label for internal (intramolecular) hydrogen bonds looks like this:
 (0.123, 4720, 4764)
 freq, lig_donor_aid, lig_acceptor_aid

_lid_add_ionic(res_label, sk, already_added_res_dict, lig_noh_dict, ligand_atoms, opacity)
Static Method

  

        res_label for ionic bonds looks like this:
         (0.0148, 'B:ARG_13:NH2', 180, [4.014, -2.630, 8.924], 2357)
#        freq, prot_label, prot_aid, [prot_ xyz], lig_aid

_lid_add_hbonds(res_label, sk, already_added_res_dict, ligand_st, lig_atom_dict, lig_noh_dict, ligand_atoms, opacity)
Static Method

  

res_label for hydrogen bonds looks like this:
 (0.40, 'A:LYS_97:HZ1', 2005, [-9.87, 7.35, -35.22], 'L-FRAG_0:O16', 16)
 frequency, prot_label  prot_aid,  [xyz], lig_label,  lig_aid

_get_pair_rmsd_plot(self, val0, val1, ts, ts_max, names, ylabel='RMSD ($\\AA$)', y_inch=2.5)

 
Parameters:
  • rmsd_l0 (float) - list of RSMD values in angstroms for lambda=0
  • rmsd_l1 (float) - list of RSMD values in angstroms for lambda=1
  • ts (float) - list of simulation times for each snapshot
  • ts_max (float) - simulation time
  • names (str) - List of names that that are in the legend
  • ylabel (str) - Label that goes on the y-axis
  • y_inch (float) - height of the image returned

_generate_2d_lig_images(self)

 

Generate 2d images of the ligands. Try to align them first, or just regular 2d images, if nothing works, return a string.


Property Details [hide private]

get_rest_density_text

Get Method:
unreachable.get_rest_density_text(self)

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2015-1Schrodinger Python API
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